400 lines
22 KiB
Python
400 lines
22 KiB
Python
#!/usr/bin/env python3
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"""Build a TASSEL/FastTree exploratory population tree with allele-level QC."""
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from __future__ import annotations
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import argparse
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import gzip
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import io
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import json
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import math
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import os
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import platform
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import re
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import shlex
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import shutil
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import subprocess
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import sys
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import time
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import uuid
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from datetime import datetime, timezone
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from pathlib import Path
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from typing import Any, TextIO
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from gfa_core.genotype_context import build_population_analysis_scope_id, genotype_scope_id_for_vcf, sha256_file
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from gfa_core.population_stage_runtime import acquire_identity_lock, population_manifest_base, release_identity_lock, write_reproducibility_bundle
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STAGE = "pop_phylogeny"
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METHOD_VERSION = "tassel_phylip_fasttree_gtr.v2"
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CONTRACT_VERSION = "v1"
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IUPAC = {
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frozenset(("A", "G")): "R", frozenset(("C", "T")): "Y",
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frozenset(("G", "C")): "S", frozenset(("A", "T")): "W",
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frozenset(("G", "T")): "K", frozenset(("A", "C")): "M",
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}
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def _open_text(path: Path) -> TextIO:
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return gzip.open(path, "rt", encoding="utf-8") if path.suffix == ".gz" else path.open("r", encoding="utf-8")
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def _eligible(ref: str, alt: str) -> bool:
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return "," not in alt and len(ref) == len(alt) == 1 and ref.upper() in "ACGT" and alt.upper() in "ACGT"
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def _decode_gt(ref: str, alt: str, sample_field: str) -> str:
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gt = sample_field.split(":", 1)[0].replace("|", "/")
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tokens = gt.split("/")
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if not tokens or any(token == "." for token in tokens):
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return "N"
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if any(token not in {"0", "1"} for token in tokens):
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raise ValueError(f"Unexpected allele index in biallelic SNP genotype: {gt}")
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bases = [ref if token == "0" else alt for token in tokens]
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return bases[0] if len(set(bases)) == 1 else IUPAC[frozenset(bases)]
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def expected_alignment_from_vcf(path: Path) -> tuple[list[str], dict[str, str], dict[str, int]]:
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samples: list[str] = []
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sequences: dict[str, list[str]] = {}
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metrics = {"input_record_count": 0, "eligible_biallelic_snp_count": 0, "excluded_multiallelic_count": 0, "excluded_non_snp_count": 0}
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with _open_text(path) as handle:
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for raw in handle:
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if raw.startswith("#CHROM\t"):
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samples = raw.rstrip("\n").split("\t")[9:]
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if not samples or len(samples) != len(set(samples)):
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raise ValueError("VCF must contain unique sample IDs")
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if any(any(char.isspace() for char in sample) for sample in samples):
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raise ValueError("VCF sample IDs cannot contain whitespace for PHYLIP output")
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sequences = {sample: [] for sample in samples}
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continue
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if raw.startswith("#") or not raw.strip():
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continue
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fields = raw.rstrip("\n").split("\t")
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if len(fields) < 9 + len(samples):
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raise ValueError("VCF record has fewer sample columns than its header")
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metrics["input_record_count"] += 1
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ref, alt = fields[3].upper(), fields[4].upper()
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if "," in alt:
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metrics["excluded_multiallelic_count"] += 1
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continue
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if not _eligible(ref, alt):
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metrics["excluded_non_snp_count"] += 1
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continue
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metrics["eligible_biallelic_snp_count"] += 1
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for sample, value in zip(samples, fields[9:]):
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sequences[sample].append(_decode_gt(ref, alt, value))
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if len(samples) < 2:
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raise ValueError("Population phylogeny requires at least two samples")
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if metrics["eligible_biallelic_snp_count"] <= 0:
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raise ValueError("No eligible biallelic SNPs for phylogeny")
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return samples, {sample: "".join(sequences[sample]) for sample in samples}, metrics
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def _write_surrogate_vcf(source: Path, destination: Path, samples: list[str]) -> dict[str, str]:
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label_map = {f"S{index:06d}": sample for index, sample in enumerate(samples, start=1)}
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with _open_text(source) as src, destination.open("w", encoding="utf-8") as dst:
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for raw in src:
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if raw.startswith("#CHROM\t"):
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fields = raw.rstrip("\n").split("\t")
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dst.write("\t".join([*fields[:9], *label_map]) + "\n")
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elif raw.startswith("#"):
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dst.write(raw)
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elif raw.strip():
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fields = raw.rstrip("\n").split("\t")
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if _eligible(fields[3].upper(), fields[4].upper()):
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dst.write(raw)
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return label_map
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def _parse_phylip(path: Path) -> tuple[list[str], dict[str, str]]:
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lines = [line.strip() for line in path.read_text(encoding="utf-8").splitlines() if line.strip()]
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if not lines:
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raise ValueError("PHYLIP alignment is empty")
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try:
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sample_count, site_count = map(int, lines[0].split()[:2])
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except Exception as exc:
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raise ValueError("Invalid PHYLIP header") from exc
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body = lines[1:]
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if len(body) < sample_count:
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raise ValueError("PHYLIP alignment has too few sample rows")
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order: list[str] = []
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sequences: dict[str, str] = {}
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for line in body[:sample_count]:
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fields = line.split()
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if len(fields) < 2:
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raise ValueError("Invalid PHYLIP first block")
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label, chunk = fields[0], "".join(fields[1:])
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if label in sequences:
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raise ValueError("PHYLIP labels must be unique")
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order.append(label)
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sequences[label] = chunk.upper()
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remaining = body[sample_count:]
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for offset in range(0, len(remaining), sample_count):
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block = remaining[offset : offset + sample_count]
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if len(block) != sample_count:
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raise ValueError("Incomplete PHYLIP interleaved block")
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for label, line in zip(order, block):
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fields = line.split()
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chunk = "".join(fields[1:] if fields and fields[0] == label else fields)
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sequences[label] += chunk.upper()
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if any(len(sequence) != site_count for sequence in sequences.values()):
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raise ValueError("PHYLIP sequence lengths do not match its header")
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return order, sequences
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def _run(command: list[str], log: Path, *, env: dict[str, str] | None = None) -> None:
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result = subprocess.run(command, text=True, capture_output=True, env=env)
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log.write_text("$ " + shlex.join(command) + "\n\nSTDOUT\n" + result.stdout + "\nSTDERR\n" + result.stderr, encoding="utf-8")
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if result.returncode != 0:
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raise RuntimeError(f"Command failed with exit code {result.returncode}: {shlex.join(command)}")
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def _version(tool: Path, args: list[str]) -> str:
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result = subprocess.run([str(tool), *args], text=True, capture_output=True, timeout=30)
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text = (result.stdout + "\n" + result.stderr).strip()
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if result.returncode != 0 or not text:
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raise RuntimeError(f"Tool version probe failed: {tool}")
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return text.splitlines()[-1]
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def _tassel_version(tool: Path) -> str:
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"""Support modern `-version` and the TASSEL 5.2 legacy wrapper."""
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for probe_args in (["-version"], []):
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tool_env = dict(os.environ)
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tool_env["PATH"] = f"{tool.parent}:{tool_env.get('PATH', '')}"
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result = subprocess.run([str(tool), *probe_args], text=True, capture_output=True, timeout=30, env=tool_env)
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text = (result.stdout + "\n" + result.stderr).strip()
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if result.returncode != 0 or not text:
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continue
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match = re.search(r"tassel[-_/ ](?:version[-_/ ]?)?([0-9]+(?:\.[0-9]+)+)", text, flags=re.IGNORECASE)
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version = f"TASSEL {match.group(1)}" if match else text.splitlines()[-1]
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return f"{version}; wrapper_sha256={sha256_file(tool)}"
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raise RuntimeError(f"Tool version probe failed: {tool}")
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def _artifact(workspace: Path, path: Path, role: str, media_type: str) -> dict[str, Any]:
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if not path.is_file() or path.stat().st_size <= 0:
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raise ValueError(f"Required artifact is missing or empty: {role}")
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size = path.stat().st_size
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return {"artifact": role, "role": role, "path": str(path.relative_to(workspace)), "full_path": str(path.resolve()), "type": media_type, "size": size, "size_bytes": size, "sha256": sha256_file(path)}
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def _newick_label(value: str) -> str:
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return value if re.fullmatch(r"[A-Za-z0-9_.-]+", value) else "'" + value.replace("'", "''") + "'"
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def _publish(source: Path, destination: Path) -> None:
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temp = destination.with_name(f".{destination.name}.{os.getpid()}.publishing")
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shutil.copy2(source, temp)
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os.replace(temp, destination)
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def _circular_tree_segments(tree: Any) -> list[tuple[str, float, float, float, float]]:
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"""Return topology-preserving radial and arc segments for a parsed tree."""
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terminals = sorted(tree.get_terminals(), key=lambda tip: str(tip.name))
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angles = {tip: 2 * math.pi * index / len(terminals) for index, tip in enumerate(terminals)}
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for clade in tree.get_nonterminals(order="postorder"):
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child_angles = [angles[child] for child in clade.clades]
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angles[clade] = sum(child_angles) / len(child_angles)
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lengths = [clade.branch_length for clade in tree.find_clades() if clade.branch_length is not None]
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depths = tree.depths(unit_branch_lengths=not bool(lengths))
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segments: list[tuple[str, float, float, float, float]] = []
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for parent in tree.find_clades(order="preorder"):
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if not parent.clades:
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continue
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child_angles = [angles[child] for child in parent.clades]
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segments.append(("arc", min(child_angles), max(child_angles), depths[parent], depths[parent]))
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for child in parent.clades:
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segments.append(("radial", angles[child], angles[child], depths[parent], depths[child]))
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return segments
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def _write_plots(newick: Path, rectangular: Path, circular: Path, expected_tips: list[str]) -> dict[str, Any]:
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from Bio import Phylo
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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tree = Phylo.read(str(newick), "newick")
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tips = [tip.name for tip in tree.get_terminals()]
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if len(tips) != len(set(tips)) or set(tips) != set(expected_tips):
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raise ValueError("Tree tip set does not match VCF samples")
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lengths = [clade.branch_length for clade in tree.find_clades() if clade.branch_length is not None]
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if any(not math.isfinite(value) or value < 0 for value in lengths):
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raise ValueError("Tree contains invalid branch lengths")
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fig = plt.figure(figsize=(9, 7))
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ax = fig.add_subplot(111)
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Phylo.draw(tree, axes=ax, do_show=False)
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fig.tight_layout()
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fig.savefig(rectangular, dpi=180)
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plt.close(fig)
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depths = tree.depths(unit_branch_lengths=not bool(lengths))
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max_depth = max((depths[tip] for tip in tree.get_terminals()), default=1.0) or 1.0
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fig = plt.figure(figsize=(8, 8))
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ax = fig.add_subplot(111, projection="polar")
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for kind, theta1, theta2, radius1, radius2 in _circular_tree_segments(tree):
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if kind == "radial":
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ax.plot([theta1, theta2], [radius1, radius2], color="#4C78A8", linewidth=1)
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else:
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steps = max(8, int(abs(theta2 - theta1) * 32))
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theta = [theta1 + (theta2 - theta1) * index / steps for index in range(steps + 1)]
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ax.plot(theta, [radius1] * len(theta), color="#4C78A8", linewidth=1)
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tip_angles = {tip: 2 * math.pi * index / len(tips) for index, tip in enumerate(sorted(tree.get_terminals(), key=lambda item: str(item.name)))}
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for tip in tree.get_terminals():
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ax.text(tip_angles[tip], depths.get(tip, max_depth) + max_depth * 0.05, tip.name, fontsize=7, ha="center", va="center")
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ax.set_axis_off()
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fig.tight_layout()
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fig.savefig(circular, dpi=180)
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plt.close(fig)
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return {"tip_count": len(tips), "tip_set_matches_vcf": True, "branch_lengths_finite": True}
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def build_parser() -> argparse.ArgumentParser:
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parser = argparse.ArgumentParser(description=__doc__)
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parser.add_argument("--workspace", required=True, type=Path)
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parser.add_argument("--job-id", required=True)
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parser.add_argument("--prefix", required=True)
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parser.add_argument("--vcf", required=True, type=Path)
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parser.add_argument("--tassel", default="run_pipeline.pl", type=Path)
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parser.add_argument("--fasttree", default="FastTree", type=Path)
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parser.add_argument("--java-memory", default="5G")
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return parser
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def _resolve_tool(value: Path) -> Path:
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candidate = value.resolve() if value.is_absolute() or value.exists() else Path(shutil.which(str(value)) or "")
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if not candidate.is_file():
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raise FileNotFoundError(f"Executable not found: {value}")
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return candidate
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def main(argv: list[str] | None = None) -> int:
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args = build_parser().parse_args(argv)
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workspace = args.workspace.resolve()
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final = workspace / "final"
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final.mkdir(parents=True, exist_ok=True)
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started = datetime.now(timezone.utc)
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clock = time.monotonic()
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run_id = f"{STAGE}_{started.strftime('%Y%m%dT%H%M%SZ')}_{uuid.uuid4().hex[:8]}"
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failed = final / f"{args.prefix}.{STAGE}.failed.{run_id}.manifest.json"
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identity12 = "unresolved"
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lock_handle = None
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runner_command = [sys.executable, "-m", "apps.cli.run_pop_phylogeny", *(argv if argv is not None else sys.argv[1:])]
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parameters = {"marker_policy": "biallelic_snp", "heterozygote_policy": "iupac", "missing_symbol": "N", "fasttree_model": "gtr", "java_memory": args.java_memory}
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manifest = population_manifest_base(
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workspace=workspace, stage=STAGE, prefix=args.prefix, job_id=args.job_id,
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run_id=run_id, started=started, runner_command=runner_command,
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parameters=parameters,
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)
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try:
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vcf = args.vcf.resolve()
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samples, _expected, marker_metrics = expected_alignment_from_vcf(vcf)
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tassel, fasttree = _resolve_tool(args.tassel), _resolve_tool(args.fasttree)
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versions = {"tassel": _tassel_version(tassel), "fasttree": _version(fasttree, ["-help"]), "python": platform.python_version()}
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genotype_scope = genotype_scope_id_for_vcf(vcf)
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input_hashes = {"population_vcf": sha256_file(vcf)}
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analysis_scope = build_population_analysis_scope_id(stage=STAGE, genotype_scope_id=genotype_scope, input_artifact_hashes=input_hashes, parameters=parameters, method_version=METHOD_VERSION, contract_version=CONTRACT_VERSION, tool_versions=versions)
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identity12 = analysis_scope.split(":", 1)[1][:12]
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lock_handle = acquire_identity_lock(workspace, STAGE, args.prefix, identity12)
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manifest.update({"genotype_scope_id": genotype_scope, "analysis_scope_id": analysis_scope, "method_version": METHOD_VERSION, "contract_version": CONTRACT_VERSION, "tool_versions": versions, "inputs": [{"role": "population_vcf", "sha256": input_hashes["population_vcf"]}]})
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attempt = workspace / ".attempts" / run_id
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attempt.mkdir(parents=True, exist_ok=False)
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filtered = attempt / "biallelic_surrogate.vcf"
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label_map = _write_surrogate_vcf(vcf, filtered, samples)
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sorted_vcf = attempt / "clean.sorted.vcf.gz"
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tassel_alignment = attempt / "tassel_alignment.phy"
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sort_command = [str(tassel), f"-Xmx{args.java_memory}", "-SortGenotypeFilePlugin", "-inputFile", str(filtered), "-outputFile", str(sorted_vcf), "-fileType", "VCF"]
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export_command = [str(tassel), f"-Xmx{args.java_memory}", "-importGuess", str(sorted_vcf), "-ExportPlugin", "-saveAs", str(tassel_alignment), "-format", "Phylip_Inter"]
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tassel_env = dict(os.environ); tassel_env["PATH"] = f"{tassel.parent}:{tassel_env.get('PATH', '')}"
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_run(sort_command, attempt / "tassel_sort.log", env=tassel_env)
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_run(export_command, attempt / "tassel_export.log", env=tassel_env)
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surrogate_samples, sorted_expected, _ = expected_alignment_from_vcf(sorted_vcf)
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alignment_order, observed = _parse_phylip(tassel_alignment)
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if alignment_order != surrogate_samples or observed != sorted_expected:
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raise ValueError("TASSEL PHYLIP alignment does not match VCF REF/ALT genotypes")
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if set(alignment_order) != set(label_map):
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raise ValueError("TASSEL label set does not match the reversible label map")
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restored_alignment = attempt / "alignment.phy"
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restored_alignment.write_text(
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f"{len(samples)} {len(next(iter(observed.values())))}\n" + "".join(f"{label_map[label]} {observed[label]}\n" for label in alignment_order),
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encoding="utf-8",
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)
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newick = attempt / "tree.nwk"
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# Keep collision-free surrogate labels through FastTree. Numeric or long
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# original labels are restored only in Newick, after tree construction.
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tree_command = [str(fasttree), "-nt", "-gtr", str(tassel_alignment)]
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tree_result = subprocess.run(tree_command, text=True, capture_output=True)
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(attempt / "fasttree.log").write_text("$ " + shlex.join(tree_command) + "\n\nSTDERR\n" + tree_result.stderr, encoding="utf-8")
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if tree_result.returncode != 0 or not tree_result.stdout.strip():
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raise RuntimeError(f"FastTree failed with exit code {tree_result.returncode}")
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restored_newick = tree_result.stdout.strip()
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for surrogate, original in label_map.items():
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restored_newick = restored_newick.replace(surrogate, _newick_label(original))
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newick.write_text(restored_newick + "\n", encoding="utf-8")
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rectangular, circular = attempt / "tree_rectangular.png", attempt / "tree_circular.png"
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tree_metrics = _write_plots(newick, rectangular, circular, samples)
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alignment_qc = attempt / "alignment_qc.json"
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alignment_metrics = {**marker_metrics, "sample_count": len(samples), "alignment_site_count": len(next(iter(observed.values()))), "label_map": label_map, "alignment_matches_vcf": True, "valid_characters": sorted(set("".join(observed.values())))}
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alignment_qc.write_text(json.dumps(alignment_metrics, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
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tree_qc = attempt / "tree_qc.json"
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tree_qc.write_text(json.dumps(tree_metrics, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
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report = attempt / "report.md"
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report.write_text("# Population phylogeny\n\n- Method: biallelic SNP VCF → TASSEL Phylip_Inter → FastTree `-nt -gtr`.\n- Genotypes were independently checked against REF/ALT with IUPAC heterozygotes.\n- Scope: exploratory SNP-only tree; not ascertainment-corrected publication phylogeny.\n", encoding="utf-8")
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environment = attempt / "environment.txt"
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environment.write_text(f"python={sys.executable}\ntassel={tassel}\ntassel_version={versions['tassel']}\nfasttree={fasttree}\nfasttree_version={versions['fasttree']}\n", encoding="utf-8")
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outputs = {
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"phylogeny_alignment_phylip": (restored_alignment, "alignment.phy", "text/plain"),
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"phylogeny_newick": (newick, "tree.nwk", "text/plain"),
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"phylogeny_rectangular_plot": (rectangular, "rectangular.png", "image/png"),
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"phylogeny_circular_plot": (circular, "circular.png", "image/png"),
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"alignment_qc": (alignment_qc, "alignment_qc.json", "application/json"),
|
|
"tree_qc": (tree_qc, "tree_qc.json", "application/json"),
|
|
"report": (report, "report.md", "text/markdown"),
|
|
"environment": (environment, "environment.txt", "text/plain"),
|
|
}
|
|
stem = f"{args.prefix}.{STAGE}.{identity12}.{run_id}"
|
|
published: dict[str, tuple[Path, str]] = {}
|
|
for role, (source, suffix, media_type) in outputs.items():
|
|
destination = final / f"{stem}.{suffix}"
|
|
_publish(source, destination)
|
|
published[role] = (destination, media_type)
|
|
manifest.update({"status": "success", "metrics": {**alignment_metrics, **tree_metrics}, "commands": [sort_command, export_command, tree_command], "artifacts": {role: _artifact(workspace, path, role, media_type) for role, (path, media_type) in published.items()}})
|
|
manifest["end_time"] = datetime.now(timezone.utc).isoformat()
|
|
manifest["elapsed_sec"] = round(time.monotonic() - clock, 6)
|
|
manifest_work = attempt / "manifest.json"
|
|
_write = lambda p, value: p.write_text(json.dumps(value, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
|
|
_write(manifest_work, manifest)
|
|
manifest_path = final / f"{stem}.manifest.json"
|
|
write_reproducibility_bundle(
|
|
workspace=workspace, stage=STAGE, prefix=args.prefix, identity12=identity12,
|
|
run_id=run_id, runner_command=runner_command, manifest_source=manifest_work,
|
|
public_manifest=manifest_path, manifest=manifest,
|
|
environment=environment.read_text(encoding="utf-8"),
|
|
artifact_sources={role: source for role, (source, _suffix, _media) in outputs.items()},
|
|
)
|
|
_publish(manifest_work, manifest_path)
|
|
return 0
|
|
except Exception as exc:
|
|
manifest.update({"status": "failed", "artifacts": {}, "error": str(exc), "end_time": datetime.now(timezone.utc).isoformat(), "elapsed_sec": round(time.monotonic() - clock, 6)})
|
|
failed.write_text(json.dumps(manifest, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
|
|
try:
|
|
write_reproducibility_bundle(
|
|
workspace=workspace, stage=STAGE, prefix=args.prefix, identity12=identity12,
|
|
run_id=run_id, runner_command=runner_command, manifest_source=failed,
|
|
public_manifest=failed, manifest=manifest,
|
|
environment=json.dumps(manifest.get("tool_versions", {}), ensure_ascii=False),
|
|
)
|
|
except Exception as bundle_exc:
|
|
manifest["reproducibility_error"] = str(bundle_exc)
|
|
failed.write_text(json.dumps(manifest, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
|
|
print(f"ERROR: {exc}", file=sys.stderr)
|
|
return 1
|
|
finally:
|
|
release_identity_lock(lock_handle)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
raise SystemExit(main())
|